Mercurial > repos > pimarin > data_manager_fetch_plasmidfinder

<tool id="data_manager_fetch_plasmidfinder" name="plasmidfinder_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>plasmidfinder database builder</description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
      <![CDATA[
        python '$__tool_directory__/plasmidfinder_fetch_database.py'
        --db_version '$database_select'
        '$output_file'
        && cat '$output_file'
      ]]></command>
    <inputs>
        <param name="database_select" type="select" label="Database version" help="Choose a database version to download (default latest version)">
            <option value="latest" selected="true">Latest available version</option>
            <option value="2.1">V2.1_2019-08-28</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <!-- Test_2 DB 2.1 -->
        <test expect_num_outputs="1">
           <param name="database_select" value="2.1"/>
           <output name="output_file" value="plasmidfinder_test_data_manager_2.1.json">
               <assert_contents>
                   <has_text text="2019_08_28"/>
               </assert_contents>
           </output>
        </test>
    </tests>
    <help><![CDATA[
        Download plasmidfinder database from the bitbucket repository: https://bitbucket.org/genomicepidemiology/plasmidfinder_db/src/master/
    ]]></help>
    <citations>
        <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
    </citations>
</tool>
author	pimarin
date	Mon, 24 Jul 2023 10:00:33 +0000
parents	5ffc68b4ec04
children	4e933a39094f